Brazilian authorities have been accused of missing a "golden opportunity" to use the Olympic Games to improve their commitment to human rights.
It comes after at least eight people were reportedly killed in police operations in the city during the Games.
According to the Institute for Public Security of the State of Rio de Janeiro, 35 people were killed in April this year, 40 in May and 49 in June.
Home invasions and "physical and verbal" aggression has also been highlighted as authorities continue their war on the city's drugs gang.
“Brazil has lost the most important medal at play during Rio 2016: the chance to become a champion on human rights,” said Atila Roque, executive director at Amnesty International Brazil.
"The Brazilian authorities missed a golden opportunity to follow on their promises to implement public security policies to make Rio a safe city for all.
"The only way to undo some of many wrongs that took place during the Games is to ensure all killings and other human rights violations by the police are effectively investigated and that those responsible are brought to justice.”
Fifty-nine armed shootouts were reportedly registered in the metropolitan region of Rio de Janeiro in the first week of the Games.
At least 14 people were killed and another 32 were injured due to armed violence over the same period, according to data collected by Cross-Fire, an app launched by Amnesty International in July to track gun violence in the favelas.
Tear gas and stun grenade have also been used by police to curb supposedly peaceful protests during the Games.
“We ended the Olympic Games with even more militarised public security policies, focused on a very selective repression, excessive use of force and combat-like police operations in favelas," added Roque.
"The outcome has been clear - a rising death toll and other human rights violations of the residents, especially young black men."
“Once again, the legacy of a major sporting event in Brazil has been tainted by police killings and abuses against peaceful protesters.
"The International Olympic Committee (IOC) and other sport organising bodies must not allow these events to be held at the expense of people’s human rights.”
Security has been a major challenge throughout the Games.
Numerous athletes, officials and spectators have been mugged over the last three weeks.
Two bullets were also fired into the equestrian venue from nearby favelas, while a media bus came under fire - either from bullets or rocks - close to the main Olympic hub in Barra de Tijuca.
But police have reacted angrily against criticism of surging crime levels, particularly when four American swimmers including six-time Olympic champion Ryan Lochte were found to have fabricated reports claiming they were victims of an armed robbery.
Ireland's leading IOC official Patrick Hickey has since been arrested and held in jail in connection with an Irish ticketing scandal following a dawn raid at the Olympic Family hotel.
IOC President Thomas Bach claims the "marvellous" Olympics have produced a "new" Rio de Janeiro from what was here before.